With an aim of developing a training course in machine / deep learning for life-science and chemistry researchers, this is a compilation of relevant materials.

• Articles, reviews and tutorials
• Books
• Courses
• Resources
• References

Articles, reviews and tutorials

Year	First author	Title / Link	Journal
2021	Jimenez-Luna	Artificial intelligence in drug discovery: Recent advances and future perspectives	Expert Opinion on Drug Discovery
2021	Bender	Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 1: Ways to make an impact, and why we are not there yet	Drug Discovery Today
2020	von Lilienfeld	Retrospective on a decade of machine learning for chemical discovery	Nature Communications
2020	Lopez	Enhancing scientific discoveries in molecular biology with deep generative models	Molecular Systems Biology
2020	Cao	Ensemble deep learning in bioinformatics	Nature Machine Intelligence
2020	Kopp	Deep learning for genomics using Janggu	Nature Communications
2020	Adam	Machine learning approaches to drug response prediction: challenges and recent progress	npj Precision Oncology
2020	Schreiber	Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome	Genome biology
2020	Schreiber	Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples	Genome biology
2020	Brown	Artificial intelligence in chemistry and drug design	Journal of Computer-Aided Molecular Design
2020	van der Schaar	How artificial intelligence and machine learning can help healthcare systems respond to COVID-19	Group website
2020	Neves	Deep Learning-driven research for drug discovery: Tackling Malaria	PLOS Computational Biology
2020	Stokes	A Deep Learning Approach to Antibiotic Discovery	Cell
2020	Xu	A comprehensive review of computational prediction of genome-wide features	Briefings in Bioinformatics
2020	Walters	Assessing the impact of generative AI on medicinal chemistry	Nature Biotechnology
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2019	Schneider	Rethinking drug design in the artificial intelligence era	Nature Reviews Drug Discovery
2019	Dias	Artificial intelligence in clinical and genomic diagnostics	Genome Medicine
2019	Filipp	Opportunities for artificial intelligence in advancing precision medicine	arXiv
2019	Yang	Machine-learning-guided directed evolution for protein engineering	Nature methods
2019	Kopp	Janggu - Deep learning for genomics	bioRxiv
2019	Zhavoronkov	Deep Aging Clocks: The Emergence of AI-Based Biomarkers of Aging and Longevity	Trends in Pharmacological Sciences
2019	Mater	Deep Learning in Chemistry	J. Chem. Inf. Model.
2019	Eraslan	Deep learning: new computational modelling techniques for genomics	Nature Reviews Genetics
2019	Avsec	The Kipoi repository accelerates community exchange and reuse of predictive models for genomics
2019	Xu	Machine learning and complex biological data
2019	Vamathevan	Applications of machine learning in drug discovery and development
2019	Preuer	Interpretable Deep Learning in Drug Discovery
2019	Polykovskiy	Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models
2019	Schneider	Mind and machine in drug design
2019	Elton	Deep learning for molecular generation and optimization-a review of the state of the art
2019	Topol	High-performance medicine: the convergence of human and artificial intelligence
2019	Gromski	How to explore chemical space using algorithms and automation
2019	Li	Deep learning in bioinformatics: introduction, application, and perspective in big data era
2019	Zachary	Machine-Learning-Assisted Directed Protein Evolution with Combinatorial Libraries
2019	Haghighatlari	Advances of Machine Learning in Molecular Modeling and Simulation
2019	PLOS	Collection in Machine Learning in Health and Biomedicine
2019	Jaganathan	Predicting Splicing from Primary Sequence with Deep Learning
2019	He	The practical implementation of artificial intelligence technologies in medicine
2019	Kriegescorte	Neural network models and deep learning - a primer for biologists
2019	Esteva	A guide to deep learning in healthcare
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2018	Yu	Visible Machine Learning for Biomedicine	Cell
2018	Brown	GuacaMol: Benchmarking Models for de Novo Molecular Design	J. Chem. Inf. Model.
2018	Sellwood	Artificial intelligence in drug discovery
2018	Yu	Artificial intelligence in healthcare
2018	Pérez	Simulations meet machine learning in structural biology
2018	Zou	A primer on deep learning in genomics
2018	Ching	Opportunities and obstacles for deep learning in biology and medicine
2018	Greene	Opportunities and obstacles for deep learning in biology and medicine
2018	Wainberg	Deep learning in biomedicine
2018	Zitnik	Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities
2018	Telenti	Deep learning of genomic variation and regulatory network data
2018	Yue	Deep Learning for Genomics: A Concise Overview
2018	Camacho	Next-Generation Machine Learning for Biological Networks
2018	Jung	Machine Learning: Basic Principles
2018	Chen	The rise of deep learning in drug discovery. A summary of the latest applications of deep learning to bioactivity and reaction predictions, and image analysis
2018	Lo	Machine learning in chemoinformatics and drug discovery
2018	Segler	Planning chemical syntheses with deep neural networks and symbolic AI
2018	Sundaram	Predicting the clinical impact of human mutation with deep neural networks
2018	Zhou	Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk
2018	Teschendorff	Avoiding common pitfalls in machine learning omic data science
2018	Colwell	Statistical and machine learning approaches to predicting protein–ligand interactions
2018	Yang	Machine learning in protein engineering
2018	Coley	Machine Learning in Computer-Aided Synthesis Planning
2018	Goh	Deep Learning for Computational Chemistry
2018	Wu	MoleculeNet: a benchmark for molecular machine learning
2018	Salim	Synthetic Patient Generation: A Deep Learning Approach Using Variational Autoencoders
2018	Butler	Machine learning for molecular and materials science
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2017	Altae-Tran	Low Data Drug Discovery with One-Shot Learning. Learning with little data in drug discovery
2017	Ransundar	Is Multitask Deep Learning Practical for Pharma?
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2016	Angermueller	Deep learning for computational biology
2016	Mamoshina	Applications of Deep Learning in Biomedicine
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2015	Park	Deep learning for regulatory genomics
2015	LeCun	Deep learning

Other:

• de la Vega de León (r), Effect of missing data on multitask prediction methods
• Liu, Deep EHR: Chronic Disease Prediction Using Medical Notes
• Radovic, Machine learning at the energy and intensity frontiers of particle physics
• Ryan, Crystal Structure Prediction via Deep Learning
• Sanchez-Lengeling and Aspuru-Guzik, Inverse molecular design using machine learning: Generative models for matter engineering
• Way, Discovering pathway and cell-type signatures in transcriptomic compendia with machine learning
• Chen, XGBoost: A Scalable Tree Boosting System
• Vinyals, Matching Networks for One Shot Learning: learning with little data
• Simm, Macau: Scalable Bayesian Multi-relational Factorization with Side Information using MCMC

Books

Authors	Title / Link
Nielsen	Neural Networks and Deep Learning
James, Witten, Hastie and Tibshirani	An Introduction to Statistical Learning with Applications in R
Hastie, Tibshirani and Friedman	The Elements of Statistical Learning: Data Mining, Inference, and Prediction
Goodfellow, Bengio and Courville	Deep Learning

Courses

Provider	Title / Link
Parr and Howard	How to explain gradient boosting
Machine learning for kids	projects
Data flair	Machine learning tutorials and Artificial Intelligence tutorials
MIT	Introduction to Deep Learning
fast.ai	Deep learning and machine learning courses
Coursera	Deep Learning Specialization
University of Cambridge	An Introduction to Machine Learning: github and book
Data School	In-depth introduction to machine learning in 15 hours of expert videos
Shirin Glander	Introduction to Machine Learning with R

Resources

Implementations:

Language	Library	Description
Python	scikit-learn	machine learning
Python	PyTorch	deep learning, Facebook
Python	Keras	deep learning
Python	TensorFlow	deep learning, Google
Python	Theano	deep learning
Python	DragoNN	deep learning for genomics
Python	Macau	Bayesian factorization
R	h2o	machine and deep learning
R	mlr	machine learning
R	caret	machine learning
R	randomForest	Breiman and Cutler's Random Forests for Classification and Regression
Java	WEKA	machine learning

Repositories:

Title / Link	Description
Kipoi	machine and deep learning models in genomics

Blogs:

• Primer for Learning Google Colab
• Scikit-Learn: A silver bullet for basic machine learning
• How to build your own Neural Network from scratch in Python
• Every single Machine Learning course on the internet, ranked by your reviews

Cheat sheets:

• 101 Machine Learning Algorithms for Data Science with Cheat Sheets
• Essential cheat sheets for deep learning and machine learning researchers
• RStudio Machine Learning Modelling
• RStudio Deep Learning with Keras
• RStudio caret package
• RStudio mlr package
• RStudio h2o environment

CRAN Task Views:

• Machine Learning & Statistical Learning

References

• Pimentel's collection of deep learning papers